Project Description:
Red crown rot is a soilborne fungal disease that is new to Illinois. Where it has been detected, significant yield reductions were recorded. Management information for our producers is lacking. In this second year of the project we will replicate work from 2020 and expand our ability to detect the pathogen by designing a molecular tool for diagnosis.

Summary/Project Scope:
Proposal Description and Background

Problem Statement
Calonectria species (asexual morph previously known as Cylindrocladium (Cy.)) are widely distributed around the world and cause diseases on a broad range of host plants in tropical and subtropical climates [1-3]. In soybeans, a disease known as red crown rot (RCR) is caused by the fungal pathogen Calonectria ilicicola [4, 5]. The fungus persists in soil and soybean residue as resistant fungal structures (microsclerotia) and fungal threads (hyphae). Following warm, wet weather, exudates from germinating seeds and roots signal the pathogen to colonize roots and root nodules, causing root decay. Under optimal conditions, stand losses due to seedling blight can occur. As the crops mature, the fungus will continue to colonize the roots and lower stem [6, 7]. Later in crop development, the fungus may produce a toxin, which moves through the water conducting vessels of the plant (xylem) to the leaves, where they accumulate and cause the foliage to develop interveinal chlorosis, necrosis, and drop from the plant [8, 9]. Reduction in photosynthetic area, coupled with reduced water and nutrient uptake resulting from occlusion of xylem, reduces grain fill, crop development, and yield. Affected plants senesce prematurely and often will contain characteristic red, ball like structures on the lower stem and crown (Figure 2). These structures, known as perithecia, contain spores of the fungus [10]. Spores are not known to play a major role in disease dissemination or infection of soybeans [11].

The fungus was first detected in the United States in 1965 in peanut and is currently widespread in southern peanut production systems, where it causes a disease known as Cylindrocladium black rot [12]. The fungus has a broad host range, and can infect several hosts including blueberry, sweetgum, yellow poplar, red oak, Ginko, clover, partridge pea, sicklepod, beggarweed, Camellia, and Eucalyptus [13]. In the United States, distribution has been limited to southern states where widespread yield losses are rare but significant local epidemics can occur, and losses can approach 50% [5, 14].

In 2018, producer near Pittsfield, IL, indicated that they had a field suffering from SDS. Upon closer examination, it was evident that the disease was caused by C. ilicicola. Isolates were collected, and Koch’s postulates confirmed [15]. Subsequent trials in 2019 showed that the pathogen can survive winters in Illinois (Kleczewski unpublished). Given the severity and extent of the damage to the fields in question, and the soilborne nature of the pathogen, we suspect that the organism has been present at that location for multiple years. How RCR arrived in Illinois and if this is similar or different from C. ilicicola populations in the southern USA is unknown.

RCR poses a threat to Illinois soybean producer productivity because 1) the distribution in IL and subsequent risk is not known as it can be misdiagnosed as SDS; 2) No resistance to RCR is available in soybean cultivars; 3) The efficacy and utility of fungicide seed treatments for managing RCR is unknown. To reduce potential losses and track disease incidence, these activities must be undertaken.

1) Survey Illinois soybeans for RCR to determine distribution and potential acreage affected

2) Screen multiple commercially available soybean fungicide seed treatments for utility in managing RCR and protecting yield

3)Develop a RCR specific molecular tool to aid in future management work

Proposed Methods/Tactics



Fields with interveinal chlorosis starting at the reproductive stage in growth will be targeted for sampling. Plant samples will be acquired at R5/R6 from each field, and sent to the Kleczewski lab, where they will be processed for presence of the pathogen following established protocols. A second season of the survey will be beneficial, as environmental conditions can mask disease symptoms from year to year, and fields infested with the pathogen may not be planted to soybeans during the first season.

Soybean seed treatments to screen for efficacy against RCR again in year 2, to increase the robustness of the data and account for environmental impacts on disease in field trials. Screening will occur in the greenhouse and microplots to assess their ability to reduce seedling blight and plant growth, and reduce foliar symptoms. A larger scale on farm study for will be conducted at a field in Pittsfield where the disease is established, allowing us to obtain yields and inoculate the site. All trials will be replicated and randomized, and data statistically analyzed.


The RCR pathogen, Calonectria ilicicola is a fungus with a broad host range and typically is found in warm regions where peanuts are produced in rotation with soybeans. Calonectria spp. are also important pathogens of ornamental legumes and trees (e.g. boxwood blight). Previous studies have used the internal transcribed region to generate species specific primers for detection of other speciesw of Calonectria on eucalyptus, and avocado [16] and due to the widespread capacity for members of the genus to cause disease on economically important legumes, online databases such as GenBank contain an abundance of Calonectria sequence data. Consequently, we can utilize sequence data from our isolates, vouchers from the USDA Mycology collection housed in Peoria, IL and online sources to develop a set of species-specific primers for use in detecting and quantifying C. ilicicola from plant tissues and soils. We will first focus on the internal transcribed region of the ribosomal DNA (rDNA) subunit, as this has been used in previous work to detect specific members of the genus. Primer sets will be designed using online primer design tools, and tested against a set of Calonectria DNA acquired via the USDA mycology collection, UIUC herbarium, and samples acquired from colleagues in other states and regions for specificity. The method will be tested on both infected plants and Calonectria-amended soil to confirm its utility, and sent to colleagues for confirmation.

Timeline:

Quarter One activities: Begin planning 2021 field season. Request seed and chemical treatments. Request Calonectria vouchers.

Quarter Two activities: Receive materials for field season. Plan field season layout. Start greenhouse trial. Start tool development.

Quarter Three activities: Plant field experiments and microplots. Rate trials. Test tool. Present study and preliminary data at field days

Quarter Four activities: Maintain field experiments. Collect data. organize survey (year 1).

Evidence of need

The confirmation of red crown rot in Illinois is problematic for several reasons. First, because this disease is new in the state, and we do not understand how similar or different it may be to populations in the south, management recommendations are absent for Illinois producers. In fact, there are no fungicides or fungicide seed treatments labeled for red crown rot in soybeans. Furthermore, there are no resistant varieties for managing this disease. Lastly, because the disease produces symptoms similar to other, more well known diseases such as SDS, it is possible that RCR has been misdiagnosed in recent years and poses a larger threat than we think. It therefore is essential that we work to address management and educational gaps at the current point in time, before the disease potentially establishes itself in other areas.

The proposed research will help maintain productivity and profitability of soybean producers in Illinois. Although losses of 25 bu/A may be extreme, any additional production losses under the current economic climate need to be minimized. Furthermore, producers need to know what practices work, in order to maximize the impacts of inputs and productivity. Working to address this issue in small, digestible parts, as propose, will enable us to provide our clientele with a reputable set of data and tools to help avoid potential losses due to RCR in the future.